On 8 June 2020 at 21:25, Paul Gevers wrote: | Source: r-base, r-cran-data.table | Control: found -1 r-base/4.0.1-1 | Control: found -1 r-cran-data.table/1.12.8+dfsg-1 | Severity: serious | Tags: sid bullseye | X-Debbugs-CC: [email protected] | User: [email protected] | Usertags: breaks needs-update | | Dear maintainer(s), | | With a recent upload of r-base the autopkgtest of r-cran-data.table | fails in testing when that autopkgtest is run with the binary packages | of r-base from unstable. It passes when run with only packages from | testing. In tabular form: | | pass fail | r-base from testing 4.0.1-1 | r-cran-data.table from testing 1.12.8+dfsg-1 | versioned deps [0] from testing from unstable | all others from testing from testing | | I copied some of the output at the bottom of this report. | | Currently this regression is blocking the migration of r-base to testing | [1]. Due to the nature of this issue, I filed this bug report against | both packages. Can you please investigate the situation and reassign the | bug to the right package?
The "'origin' must be supplied" message makes it *extremely* likely that is in fact a change made by R 4.0.0. R is released once a year as a new minor (plus patch releases) and *extremely* carefully vetted / prepared (and folks who upload packages to CRAN always test against the coming version. So the data.table team upstream surely had this fixed as well. The _released_ version of data.table still has the problem too as we can see at CRAN: https://cloud.r-project.org/web/checks/check_results_data.table.html I would expect the next version to be fixed. In the mean time the bug could be fixed in the test(s), or the tests could be (temporarily) suspended. (I had a quick look at the code around tests 1390.* (in file inst/tests/tests.Raw) but didn't immediately come up with a fix. Dirk | | More information about this bug and the reason for filing it can be found on | https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation | | Paul | | [0] You can see what packages were added from the second line of the log | file quoted below. The migration software adds source package from | unstable to the list if they are needed to install packages from | r-base/4.0.1-1. I.e. due to versioned dependencies or breaks/conflicts. | [1] https://qa.debian.org/excuses.php?package=r-base | | https://ci.debian.net/data/autopkgtest/testing/amd64/r/r-cran-data.table/5803495/log.gz | | BEGIN TEST main.R | | R version 4.0.1 (2020-06-06) -- "See Things Now" | Copyright (C) 2020 The R Foundation for Statistical Computing | Platform: x86_64-pc-linux-gnu (64-bit) | | R is free software and comes with ABSOLUTELY NO WARRANTY. | You are welcome to redistribute it under certain conditions. | Type 'license()' or 'licence()' for distribution details. | | R is a collaborative project with many contributors. | Type 'contributors()' for more information and | 'citation()' on how to cite R or R packages in publications. | | Type 'demo()' for some demos, 'help()' for on-line help, or | 'help.start()' for an HTML browser interface to help. | Type 'q()' to quit R. | | > require(data.table) | Loading required package: data.table | > | > test.data.table() # runs the main test suite of 5,000+ tests in | /inst/tests/tests.Rraw | getDTthreads(verbose=TRUE): | omp_get_num_procs() 2 | R_DATATABLE_NUM_PROCS_PERCENT unset (default 50) | R_DATATABLE_NUM_THREADS unset | omp_get_thread_limit() 2147483647 | omp_get_max_threads() 2 | OMP_THREAD_LIMIT unset | OMP_NUM_THREADS unset | RestoreAfterFork true | data.table is using 1 threads. See ?setDTthreads. | test.data.table() running: | /usr/lib/R/site-library/data.table/tests/tests.Rraw.bz2 | | **** Suggested package bit64 is not installed. Tests using it will be | skipped. | | | **** Suggested package xts is not installed. Tests using it will be skipped. | | | **** Suggested package nanotime is not installed. Tests using it will be | skipped. | | | **** Suggested package R.utils is not installed. Tests using it will be | skipped. | | | **** Suggested package yaml is not installed. Tests using it will be | skipped. | | Test 1390.3 produced 1 errors but expected 0 | Expected: | Observed: 'origin' must be supplied | Test 1390.4 produced 1 errors but expected 0 | Expected: | Observed: 'origin' must be supplied | Test 1390.5 produced 1 errors but expected 0 | Expected: | Observed: 'origin' must be supplied | Test 1760 not run because this session either has no OpenMP or has been | limited to one thread (e.g. under UBSAN and ASAN) | | 10 longest running tests took 15s (38% of 40s) | ID time nTest | 1: 1888 2.860 9 | 2: 1848 1.766 1 | 3: 1874 1.753 5 | 4: 1438 1.564 354 | 5: 1912 1.530 2 | 6: 1223 1.186 728 | 7: 1648 1.171 45 | 8: 1650 1.158 45 | 9: 1652 1.143 45 | 10: 1437 1.116 36 | | Error in test.data.table() : | 3 errors out of 7311 in 40.4s elapsed (38.2s cpu) on Sun Jun 7 | 09:33:45 2020. [endian==little, sizeof(long double)==16, | sizeof(pointer)==8, TZ=Etc/UTC, locale='C', l10n_info()='MBCS=FALSE; | UTF-8=FALSE; Latin-1=FALSE', getDTthreads()='omp_get_num_procs()==2; | R_DATATABLE_NUM_PROCS_PERCENT==unset (default 50); | R_DATATABLE_NUM_THREADS==unset; omp_get_thread_limit()==2147483647; | omp_get_max_threads()==2; OMP_THREAD_LIMIT==unset; | OMP_NUM_THREADS==unset; RestoreAfterFork==true; data.table is using 1 | threads. See ?setDTthreads.']. Search tests/tests.Rraw.bz2 for test | numbers: 1390.3, 1390.4, 1390.5. | In addition: Warning messages: | 1: In parse(n = -1, file = file, srcfile = NULL, keep.source = FALSE) : | invalid input found on input connection | '/usr/lib/R/site-library/data.table/tests/tests.Rraw.bz2' | 2: In parse(n = -1, file = file, srcfile = NULL, keep.source = FALSE) : | invalid input found on input connection | '/usr/lib/R/site-library/data.table/tests/tests.Rraw.bz2' | Execution halted | autopkgtest [09:33:45]: test run-unit-test: -----------------------] | | x[DELETED ATTACHMENT signature.asc, application/pgp-signature] -- http://dirk.eddelbuettel.com | @eddelbuettel | [email protected]
